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🧮 Math, table support in myst-to-jats
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@fwkoch
fwkoch committed Nov 16, 2023
1 parent af0ff8d commit 52fc293
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Showing 4 changed files with 139 additions and 74 deletions.
5 changes: 5 additions & 0 deletions .changeset/funny-lies-arrive.md
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@@ -0,0 +1,5 @@
---
'jats-to-myst': patch
---

Math, table, additional tweaks for jats-to-myst
22 changes: 20 additions & 2 deletions package-lock.json
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6 changes: 4 additions & 2 deletions packages/jats-to-myst/package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,10 @@
"url": "https://github.com/executablebooks/mystmd/issues"
},
"dependencies": {
"doi-utils": "^2.0.0",
"doi-utils": "^2.0.2",
"jats-tags": "^1.0.8",
"jats-xml": "^1.0.8",
"mathml-to-latex": "^1.3.0",
"myst-common": "^1.1.11",
"myst-frontmatter": "^1.1.11",
"myst-spec": "^0.0.4",
Expand All @@ -48,7 +49,8 @@
"unist-util-select": "^4.0.3",
"unist-util-remove": "^3.1.0",
"vfile": "^5.0.0",
"vfile-reporter": "^7.0.4"
"vfile-reporter": "^7.0.4",
"xml-js": "^1.6.11"
},
"devDependencies": {
"myst-to-tex": "^1.0.10"
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180 changes: 110 additions & 70 deletions packages/jats-to-myst/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@ import { u } from 'unist-builder';
import { RefType } from 'jats-tags';
import { Jats } from 'jats-xml';
import { keysTransform } from 'myst-transforms';
import { MathMLToLaTeX } from 'mathml-to-latex';
import { js2xml } from 'xml-js';
import type { Handler, IJatsParser, JatsResult, Options, StateData } from './types.js';
import { basicTransformations } from './transforms/index.js';

Expand All @@ -28,6 +30,38 @@ function refTypeToReferenceKind(kind?: RefType): string | undefined {
}
}

function texMathFromNode(node: GenericNode) {
const texMath = select('tex-math', node) as GenericNode;
if (texMath && texMath.children?.[0].cdata) {
return texMath.children?.[0].cdata;
}
selectAll('*', node).forEach((n: any) => {
if (n.type.startsWith('mml:')) {
n.type = n.type.substring(4);
}
});
const math = select('math', node) as GenericNode;
if (!math) return;
[math, ...selectAll('math *', node)].forEach((n: any) => {
const { type, value, children, ...attributes } = n;
if (type === 'text') {
n.type = 'text';
n.text = value;
delete n.value;
} else {
n.type = 'element';
n.name = type;
n.elements = children;
n.attributes = attributes;
delete n.children;
Object.keys(attributes).forEach((k) => {
delete n[k];
});
}
});
return MathMLToLaTeX.convert(js2xml({ type: 'element', name: 'root', elements: [math] }));
}

type Attributes = Record<string, any>;

const handlers: Record<string, Handler> = {
Expand Down Expand Up @@ -83,26 +117,30 @@ const handlers: Record<string, Handler> = {
// // The use of thematic breaks should be restricted to use inside table cells.
// // https://jats.nlm.nih.gov/archiving/tag-library/1.3/element/hr.html
// },
// ['inline-formula'](node, state) {
// // state.openNode('inline-formula');
// // state.openNode('tex-math');
// // state.addLeaf('cdata', { cdata: node.value });
// // state.closeNode();
// // state.closeNode();
// },
// ['disp-formula'](node, state) {
// const { identifier, enumerated, enumerator } = node;
// state.openNode('disp-formula', { id: identifier });
// if (enumerated !== false && enumerator) {
// state.openNode('label');
// state.text(`(${enumerator})`);
// state.closeNode();
// }
// state.openNode('tex-math');
// state.addLeaf('cdata', { cdata: node.value });
// state.closeNode();
// state.closeNode();
// },
['inline-formula'](node, state) {
const texMath = texMathFromNode(node);
if (texMath) {
state.addLeaf('inlineMath', {
value: texMath,
label: node.id,
identifier: node.id,
});
} else {
state.renderChildren(node);
}
},
['disp-formula'](node, state) {
const texMath = texMathFromNode(node);
if (texMath) {
state.addLeaf('math', {
value: texMath,
label: node.id,
identifier: node.id,
});
} else {
state.renderChildren(node);
}
},
// mystRole(node, state) {
// state.renderChildren(node);
// },
Expand Down Expand Up @@ -159,29 +197,6 @@ const handlers: Record<string, Handler> = {
// // This is used inside of disp-quotes
// state.renderInline(node, 'attrib');
// },
// table(node, state) {
// state.renderInline(node, 'table');
// },
// tableHead(node, state) {
// state.renderInline(node, 'thead');
// },
// tableBody(node, state) {
// state.renderInline(node, 'tbody');
// },
// tableFooter(node, state) {
// state.renderInline(node, 'tfoot');
// },
// tableRow(node, state) {
// state.renderInline(node, 'tr');
// },
// tableCell(node, state) {
// const { align, colspan, rowspan } = node as TableCell;
// state.renderInline(node, node.header ? 'th' : 'td', {
// align,
// colspan: colspan ? String(colspan) : undefined,
// rowspan: rowspan ? String(rowspan) : undefined,
// });
// },
// image(node, state) {
// if (node.url?.startsWith('http')) {
// state.warn(`Image URL is remote (${node.url})`, node, 'image');
Expand Down Expand Up @@ -210,34 +225,10 @@ const handlers: Record<string, Handler> = {
const caption = select('caption', node) as GenericNode;
const graphic = select('graphic', node) as GenericNode;
const title = select('title', node) as GenericNode;
state.openNode('container', { label: node.id, identifier: node.id });
state.openNode('container', { label: node.id, identifier: node.id, kind: 'figure' });
const link = graphic?.['xlink:href'];
if (state.jats.source?.includes('elifesciences')) {
const elifeId = state.jats.doi?.split('/')[1].split('.')[1];
state.addLeaf('image', {
url: `https://iiif.elifesciences.org/lax:${elifeId}/${link}/full/617,/0/default.png`,
urlOptimized: `https://iiif.elifesciences.org/lax:${elifeId}/${link}/full/617,/0/default.webp`,
});
} else if (state.jats.source?.includes('joss')) {
const jossId = state.jats.doi?.split('/')[1].split('.')[1];
state.addLeaf('image', {
url: `https://raw.githubusercontent.com/openjournals/joss-papers/master/joss.${jossId}/${link}`,
});
} else if (state.jats.source?.includes('https://journals.plos.org')) {
// from: info:doi/10.1371/journal.pmed.1004118.g001
// to: https://journals.plos.org/plosmedicine/article/figure/image?size=inline&id=10.1371/journal.pmed.1004118.g001
// size is "inline" or "large"
// e.g. "plosmedicine"
const journal = new URL(state.jats.source).pathname.split('/')[1];
const figureDoi = link?.replace(/^info:doi/, '');
const size = 'large';
const url = `https://journals.plos.org/${journal}/article/figure/image?size=${size}&id=${figureDoi}`;
state.addLeaf('image', { url });
} else {
const pmcid = state.jats.pmc;
state.addLeaf('image', {
url: `https://www.ncbi.nlm.nih.gov/pmc/articles/PMC${pmcid}/bin/${link}.jpg`,
});
if (link) {
state.addLeaf('image', { url: link });
}
state.openNode('caption');
if (title) {
Expand All @@ -250,6 +241,55 @@ const handlers: Record<string, Handler> = {
state.closeNode();
state.closeNode();
},
['table-wrap'](node, state) {
const caption = (select('caption', node) ?? select('lable', node)) as GenericNode;
state.openNode('container', { label: node.id, identifier: node.id, kind: 'table' });
if (caption) {
state.openNode('caption');
state.renderChildren(caption);
state.closeNode();
}
state.renderChildren(node);
state.closeNode();
},
table(node, state) {
state.openNode('table');
state.renderChildren(node);
state.closeNode();
},
thead(node, state) {
state.renderChildren(node);
},
tbody(node, state) {
state.renderChildren(node);
},
tfoot(node, state) {
state.renderChildren(node);
},
tr(node, state) {
state.openNode('tableRow');
state.renderChildren(node);
state.closeNode();
},
th(node, state) {
const { align, colspan, rowspan } = node;
state.openNode('tableCell', { header: true, align, colspan, rowspan });
state.renderChildren(node);
state.closeNode();
},
td(node, state) {
const { align, colspan, rowspan } = node;
state.openNode('tableCell', { align, colspan, rowspan });
state.renderChildren(node);
state.closeNode();
},
break(node, state) {
state.addLeaf('break');
},
['named-content'](node, state) {
// TODO: Not just ignore things marked as named-content
state.renderChildren(node);
},
// container(node, state) {
// state.data.isInContainer = true;
// switch (node.kind) {
Expand Down

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